Hi Doug, I tried lowering delta to really low values, eg., .001, but it doesn't seem change things much. Under ideal circumstances, would I expect the space between the white and pial surfaces to be completely filled? Also, I noted the -help states that delta is relative to the thickness at each vertex if -frac is used, but am a bit unsure of what this means. Does it mean that, for eg., if the vertex thickness is 3mm, then start = 0, stop = 1, delta = 0.5 will fill the entire 3mm space in increments of 1.5mm? Whereas if -abs is specified, start = 0, stop = 1, delta = 0.5 means that the space between 0 and 1mm from the specified surface will be filled, in increments of 0.5mm? Hope this makes sense and thanks again for your help, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED]
________________________________ From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 6/12/2005 6:10 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol >From --help on mri_label2vol: --proj type start stop delta Project the label along the surface normal. type can be abs or frac. abs means that the start, stop, and delta are measured in mm. frac means that start, stop, and delta are relative to the thickness at each vertex. The label definition is changed to fill in label points in increments of delta from start to stop. Requires subject and hemi in order to load in a surface and thickness. Uses the white surface. The label MUST have been defined on the surface. Not sure why it's splotchy. Can you lower the delta? doug Fornito, Alexander wrote: I see. The ribbon actually looks like the result I got when i used mri_label2vol. So would I be correct in saying that a that using the flag -proj frac 0, 1, .1 will extract that protion of ?h.ribbon.mgz that is associated with the label? What exactly does delta (eg., .1) correspond to? How come the ribbon.mgz appears 'splotchy' (ie., the space between the white and pial surfaces is not completely filled.) Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -----Original Message----- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Sat 3/12/2005 9:43 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol This is done in the newer versions of recon all. It creates subject/mri/?h.ribbon.mgz using mri_surf2vol. Here's what recon-all does: set cmd = (mri_surf2vol --mkmask --hemi $hemi) set cmd = ($cmd --fillribbon --template orig$MGZ) set cmd = ($cmd --volregidentity $subjid --outvol $hemi.ribbon.mgz) doug On Sat, 3 Dec 2005, Fornito, Alexander wrote: Hi, I'm wandering if its possible to convert a label into a volume so that it fills the space between the white and pial surfaces used in calculating thickness. That is, if the label is drawn on the wm surface, is is possible to determine what points on the pial surface are used to calculate the thickness of that label? I've been playing with the --proj option in mr_label2vol. The --help states that --proj frac "means that start, stop, and delta are relative to the thickness at each vertex." I tried using the start, stop and delta values provided in the example (0, 1 .1), but it doesn't seem to completely fill the area between the two surfaces. I've also tried plugging in other values and can't seem to get it right.Is there soemthing I'm missing? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
